The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process.

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Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI, to the USDA processing facility at the University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics, core microbiome, differential abundance, and co-occurrence network analyses. Harvest date, finishing weight, and GIT location had a significant impact on microbial diversity and community composition (P < 0.05), and there was an interaction between GIT location and harvest date (P < 0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, with Moryella in the rumen and Acinetobacter in the hindgut emerging as the highest scoring hubs. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.IMPORTANCEWith the global rise in antimicrobial resistance and the threat of foodborne illness, determining intervention strategies prior to harvest is a promising solution. The period between transportation from the feedlot to harvest may increase the risk of foodborne illness. During this period, cattle are withheld feed to reduce gastrointestinal tract (GIT) contents during carcass dressing. Feed withdrawal has many unintended consequences, such as acidosis and an increase in GIT pathogenic bacteria, that may result in foodborne pathogens on the final product. These consequences have yet to be thoroughly investigated in dairy-beef cross cattle, which have been rising in prominence in the United States. The GIT microbiome of dairy-beef cross cattle has been scarcely characterized despite its influence on preventing the proliferation of common pathogens in the GIT. Therefore, it is necessary to determine the impacts of feed withdrawal on the GIT microbiome and its relation to foodborne illness.